merge last trunk modifications

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/alpha_complex_3d_module_vincent@3908 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: ab0fe69130ba3cbb329e0e975053809180edba5d

9 files changed, 192 insertions, 16 deletions

diff --git a/CMakeGUDHIVersion.txt b/CMakeGUDHIVersion.txt
index 6811d7e1..ebaddd47 100644
--- a/CMakeGUDHIVersion.txt
+++ b/CMakeGUDHIVersion.txt
@@ -1,5 +1,5 @@
 set (GUDHI_MAJOR_VERSION 2)
-set (GUDHI_MINOR_VERSION 2)
+set (GUDHI_MINOR_VERSION 3)
 set (GUDHI_PATCH_VERSION 0)
 set(GUDHI_VERSION ${GUDHI_MAJOR_VERSION}.${GUDHI_MINOR_VERSION}.${GUDHI_PATCH_VERSION})
 
diff --git a/data/points/human.COPYRIGHT b/data/points/human.COPYRIGHT
new file mode 100644
index 00000000..cb9bdb59
--- /dev/null
+++ b/data/points/human.COPYRIGHT
@@ -0,0 +1,77 @@
+The human.off point cloud is available at this webpage :
+http://segeval.cs.princeton.edu/
+
+LICENSE
+=======
+
+AIM@SHAPE General License for Shapes
+Applicable terms
+----------------
+
+This is the general AIM@SHAPE license applicable to models in the
+Shape Repository. It should be noted that each model is a
+representation of, and is distinct from, a shape, whether physical or
+imaginary. While the shape may be subject to its own terms, the terms
+governing the model you are about to download are described herein.
+
+For some models, the owners have defined specific licenses. The terms
+and conditions laid down in these licenses are in addition to the
+terms prescribed here, and are to be adhered to strictly when using
+such models.
+
+Acknowledgements
+----------------
+
+When including models from the Shape Repository in your website or
+research work, or when using them for other purposes allowed by the
+terms described herein, the AIM@SHAPE project and the model owner must
+be acknowledged as the sources of the models, for example with the
+phrase, "... model is provided courtesy of <model_owner> by the
+AIM@SHAPE Shape Repository."
+
+Information on <model_owner> is present in the accompanying metadata
+files and, where present, owner licenses.
+
+Metadata
+--------
+
+Each model is accompanied by its metadata file. Please keep this file
+with the model as it contains important information about the
+model. Please let us know if you find any errors in the metadata.
+
+(Im)proper use
+--------------
+
+Some models in the Shape Repository represent artifacts of religious,
+cultural and/or historical significance, e.g. the Max Planck
+model. Such models have been entrusted to the Shape Repository under
+the hope that they will be used respectfully and
+conscientiously. Please refrain from conducting experiments on them
+that may be rash or insensitive to people's feelings. Such experiments
+include, but are not limited to, morphing, animation, boolean
+operations, simulations of burning, breaking, exploding and melting.
+
+Models in the Shape Repository are made freely available for research
+and non-commercial purposes only. Use of these models for commercial
+purposes is permitted only after the express approval of the Shape
+Repository and the onwner has been obtained. Please contact us using
+the webform on our site in this regard.
+
+
+CITATION
+========
+
+If you use any part of this benchmark, please cite:
+Xiaobai Chen, Aleksey Golovinskiy, and Thomas Funkhouser,
+A Benchmark for 3D Mesh Segmentation
+ACM Transactions on Graphics (Proc. SIGGRAPH), 28(3), 2009.
+
+@article{Chen:2009:ABF,
+  author = "Xiaobai Chen and Aleksey Golovinskiy and Thomas Funkhouser",
+  title = "A Benchmark for {3D} Mesh Segmentation",
+  journal = "ACM Transactions on Graphics (Proc. SIGGRAPH)",
+  year = "2009",
+  month = aug,
+  volume = "28",
+  number = "3"
+}
\ No newline at end of file
diff --git a/scripts/create_gudhi_version.sh b/scripts/create_gudhi_version.sh
new file mode 100755
index 00000000..0b393980
--- /dev/null
+++ b/scripts/create_gudhi_version.sh
@@ -0,0 +1,59 @@
+#!/bin/bash
+
+login="vrouvrea"
+version="2.3.0.rc3"
+cgaldir="/home/vincent/workspace/CGAL-4.11-HO/build"
+cpucount=7
+
+
+# We start from scripts dir in the dev branch
+cd ..
+RELATIVEURL=`svn info . |grep -F "Relative URL:" | awk '{print $NF}'`
+
+if [ "$RELATIVEURL" != "^/trunk" ]
+then
+echo "Script must be launched in trunk and not in $RELATIVEURL"
+exit
+fi
+
+rm -rf build; mkdir build; cd build; cmake  -DCMAKE_BUILD_TYPE=Debug -DDEBUG_TRACES=ON -DCGAL_DIR=${cgaldir} -DWITH_GUDHI_EXAMPLE=ON -DWITH_GUDHI_BENCHMARK=ON -DPython_ADDITIONAL_VERSIONS=3 ..
+cmake  -DCMAKE_BUILD_TYPE=Debug .
+
+make -j ${cpucount} all test
+
+cd ..
+svn st | grep -v GUDHIVersion.cmake | grep "^\?" | awk "{print \$2}" | xargs rm -rf
+
+svn copy svn+ssh://${login}@scm.gforge.inria.fr/svnroot/gudhi/trunk svn+ssh://${login}@scm.gforge.inria.fr/svnroot/gudhi/tags/gudhi-release-${version} \
+  -m "Creating a tag of Gudhi release version ${version}."
+
+cd build
+make user_version
+
+userversiondir=`find . -type d -name "*_GUDHI_${version}" | sed 's/\.\///g'`
+echo "User version directory = ${userversiondir}"
+
+tar -czvf ${userversiondir}.tar.gz ${userversiondir}
+
+userdocdir=${userversiondir/GUDHI/GUDHI_DOC}
+echo "User documentation directory = ${userdocdir}"
+mkdir ${userdocdir}
+make doxygen
+
+cp -R ${userversiondir}/doc/html ${userdocdir}/cpp
+cd ${userversiondir}
+rm -rf build; mkdir build; cd build; cmake  -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=./installed -DCGAL_DIR=${cgaldir} -DWITH_GUDHI_EXAMPLE=ON -DPython_ADDITIONAL_VERSIONS=3 ..
+make sphinx
+
+cp -R cython/sphinx ../../${userdocdir}/python
+cd ../..
+tar -czvf ${userdocdir}.tar.gz ${userdocdir}
+
+cd ${userversiondir}/build
+make -j ${cpucount} all test install
+
+cd ../..
+actualdir=`pwd`
+echo "Library is available at ${actualdir}/${userversiondir}.tar.gz"
+sha256sum ${userversiondir}.tar.gz
+echo "Documentation is available at ${actualdir}/${userdocdir}.tar.gz"
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index c60346d5..6c446104 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -71,7 +71,7 @@ export(PACKAGE GUDHI)
 
 message("++ make install will install ${PROJECT_NAME} in the following directory : ${CMAKE_INSTALL_PREFIX}")
 # Create the GUDHIConfig.cmake and GUDHIConfigVersion files
-set(CONF_INCLUDE_DIRS "${CMAKE_INSTALL_PREFIX}/include")
+set(CONF_INCLUDE_DIRS "${CMAKE_SOURCE_DIR}/include;${CMAKE_INSTALL_PREFIX}/include")
 configure_file(GUDHIConfig.cmake.in "${PROJECT_BINARY_DIR}/GUDHIConfig.cmake" @ONLY)
 configure_file(GUDHIConfigVersion.cmake.in "${PROJECT_BINARY_DIR}/GUDHIConfigVersion.cmake" @ONLY)
 
diff --git a/src/GUDHIConfig.cmake.in b/src/GUDHIConfig.cmake.in
index 02b540dc..8d82f235 100644
--- a/src/GUDHIConfig.cmake.in
+++ b/src/GUDHIConfig.cmake.in
@@ -1,7 +1,12 @@
 # - Config file for the GUDHI package
 # It defines the following variables
 #  GUDHI_INCLUDE_DIRS - include directories for GUDHI
+#
+# Order is :
+# 1. user defined GUDHI_INCLUDE_DIRS
+# 2. ${CMAKE_SOURCE_DIR}/include     => Where the 'cmake' has been done
+# 3. ${CMAKE_INSTALL_PREFIX}/include => Where the 'make install' has been performed
 
 # Compute paths
-set(GUDHI_INCLUDE_DIRS "@CONF_INCLUDE_DIRS@")
+set(GUDHI_INCLUDE_DIRS "${GUDHI_INCLUDE_DIRS};@CONF_INCLUDE_DIRS@")
 
diff --git a/src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h b/src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h
index c68b5c0b..c51e47a5 100644
--- a/src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h
+++ b/src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h
@@ -300,7 +300,10 @@ class Persistent_cohomology {
     // with multiplicity. We used to sum the coefficients directly in
     // annotations_in_boundary by using a map, we now do it later.
     typedef std::pair<Column *, int> annotation_t;
-    thread_local std::vector<annotation_t> annotations_in_boundary;
+#ifdef GUDHI_CAN_USE_CXX11_THREAD_LOCAL
+    thread_local
+#endif  // GUDHI_CAN_USE_CXX11_THREAD_LOCAL
+    std::vector<annotation_t> annotations_in_boundary;
     annotations_in_boundary.clear();
     int sign = 1 - 2 * (dim_sigma % 2);  // \in {-1,1} provides the sign in the
                                          // alternate sum in the boundary.
diff --git a/src/Simplex_tree/include/gudhi/Simplex_tree.h b/src/Simplex_tree/include/gudhi/Simplex_tree.h
index ee96d5a2..3ab23c12 100644
--- a/src/Simplex_tree/include/gudhi/Simplex_tree.h
+++ b/src/Simplex_tree/include/gudhi/Simplex_tree.h
@@ -1057,7 +1057,10 @@ class Simplex_tree {
     Dictionary_it next = siblings->members().begin();
     ++next;
 
-    thread_local std::vector<std::pair<Vertex_handle, Node> > inter;
+#ifdef GUDHI_CAN_USE_CXX11_THREAD_LOCAL
+    thread_local
+#endif  // GUDHI_CAN_USE_CXX11_THREAD_LOCAL
+    std::vector<std::pair<Vertex_handle, Node> > inter;
     for (Dictionary_it s_h = siblings->members().begin();
          s_h != siblings->members().end(); ++s_h, ++next) {
       Simplex_handle root_sh = find_vertex(s_h->first);
diff --git a/src/common/doc/installation.h b/src/common/doc/installation.h
index d36a216f..ab54cbc7 100644
--- a/src/common/doc/installation.h
+++ b/src/common/doc/installation.h
@@ -2,22 +2,34 @@
  *  \tableofcontents
  * As GUDHI is a header only library, there is no need to install the library.
  * 
- * Examples of GUDHI headers inclusion can be found in \ref demos.
+ * Examples of GUDHI headers inclusion can be found in \ref utilities.
  * 
  * \section compiling Compiling
  * The library uses c++11 and requires <a target="_blank" href="http://www.boost.org/">Boost</a>  &ge; 1.48.0
  * and <a target="_blank" href="https://www.cmake.org/">CMake</a> &ge; 3.1.
  * It is a multi-platform library and compiles on Linux, Mac OSX and Visual Studio 2015.
  * 
- * \subsection demos Demos and examples
- * To build the demos and examples, run the following commands in a terminal:
+ * \subsection utilities Utilities and examples
+ * To build the utilities, run the following commands in a terminal:
 \verbatim  cd /path-to-gudhi/
 mkdir build
 cd build/
 cmake ..
 make \endverbatim
- * A list of examples is available <a href="examples.html">here</a>.
+ * By default, examples are disabled. You can activate their compilation with
+ * <a href="https://cmake.org/cmake/help/v3.0/manual/ccmake.1.html">ccmake</a> (on Linux and Mac OSX),
+ * <a href="https://cmake.org/cmake/help/v3.0/manual/cmake-gui.1.html">cmake-gui</a> (on Windows) or y mofifying the
+ * cmake command as follows :
+\verbatim  cmake -DWITH_GUDHI_EXAMPLE=ON ..
+make \endverbatim
+ * A list of utilities and examples is available <a href="examples.html">here</a>.
  * 
+ * \subsection libraryinstallation Installation
+ * To install the library (headers and activated utilities), run the following command in a terminal:
+ * \verbatim  make install \endverbatim
+ * This action may require to be in the sudoer or administrator of the machine in function of the operating system and
+ * of <a href="https://cmake.org/cmake/help/v3.0/variable/CMAKE_INSTALL_PREFIX.html">CMAKE_INSTALL_PREFIX</a>.
+ *
  * \subsection testsuites Test suites
  * To test your build, run the following command in a terminal:
  * \verbatim  make test \endverbatim
@@ -31,6 +43,10 @@ make doxygen
 # You can customize the directory name by calling `cmake -DUSER_VERSION_DIR=/my/custom/folder`
 \endverbatim
  *
+ * \subsection helloworld Hello world !
+ * The <a target="_blank" href="https://gitlab.inria.fr/GUDHI/hello-gudhi-world">Hello world for GUDHI</a>
+ * project is an example to help developers to make their own C++ project on top of the GUDHI library.
+ *
  * \section optionallibrary Optional third-party library
  * \subsection gmp GMP
  * The multi-field persistent homology algorithm requires GMP which is a free library for arbitrary-precision
diff --git a/src/cython/CMakeLists.txt b/src/cython/CMakeLists.txt
index 1849a6ec..09ea28f1 100644
--- a/src/cython/CMakeLists.txt
+++ b/src/cython/CMakeLists.txt
@@ -130,7 +130,11 @@ if(CYTHON_FOUND)
   if(CGAL_FOUND)
     can_cgal_use_cxx11_thread_local()
     if (NOT CGAL_CAN_USE_CXX11_THREAD_LOCAL_RESULT)
-      add_gudhi_cython_lib(${Boost_THREAD_LIBRARY})
+      if(CMAKE_BUILD_TYPE MATCHES Debug)
+        add_gudhi_cython_lib("${Boost_THREAD_LIBRARY_DEBUG}")
+      else()
+        add_gudhi_cython_lib("${Boost_THREAD_LIBRARY_RELEASE}")
+      endif()
       set(GUDHI_CYTHON_LIBRARY_DIRS "${GUDHI_CYTHON_LIBRARY_DIRS}'${Boost_LIBRARY_DIRS}', ")
     endif()
     # Add CGAL compilation args
@@ -139,22 +143,26 @@ if(CYTHON_FOUND)
       set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DCGAL_HEADER_ONLY', ")
     else(CGAL_HEADER_ONLY)
       add_gudhi_debug_info("CGAL version ${CGAL_VERSION}")
-      add_gudhi_cython_lib(${CGAL_LIBRARY})
+      add_gudhi_cython_lib("${CGAL_LIBRARY}")
       set(GUDHI_CYTHON_LIBRARY_DIRS "${GUDHI_CYTHON_LIBRARY_DIRS}'${CGAL_LIBRARIES_DIR}', ")
       # If CGAL is not header only, CGAL library may link with boost system,
-      add_gudhi_cython_lib(${Boost_SYSTEM_LIBRARY})
+      if(CMAKE_BUILD_TYPE MATCHES Debug)
+        add_gudhi_cython_lib("${Boost_SYSTEM_LIBRARY_DEBUG}")
+      else()
+        add_gudhi_cython_lib("${Boost_SYSTEM_LIBRARY_RELEASE}")
+      endif()
       set(GUDHI_CYTHON_LIBRARY_DIRS "${GUDHI_CYTHON_LIBRARY_DIRS}'${Boost_LIBRARY_DIRS}', ")
     endif(CGAL_HEADER_ONLY)
     # GMP and GMPXX are not required, but if present, CGAL will link with them.
     if(GMP_FOUND)
       add_gudhi_debug_info("GMP_LIBRARIES = ${GMP_LIBRARIES}")
       set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DCGAL_USE_GMP', ")
-      add_gudhi_cython_lib(${GMP_LIBRARIES})
+      add_gudhi_cython_lib("${GMP_LIBRARIES}")
       set(GUDHI_CYTHON_LIBRARY_DIRS "${GUDHI_CYTHON_LIBRARY_DIRS}'${GMP_LIBRARIES_DIR}', ")
       if(GMPXX_FOUND)
         add_gudhi_debug_info("GMPXX_LIBRARIES = ${GMPXX_LIBRARIES}")
         set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DCGAL_USE_GMPXX', ")
-        add_gudhi_cython_lib(${GMPXX_LIBRARIES})
+        add_gudhi_cython_lib("${GMPXX_LIBRARIES}")
         set(GUDHI_CYTHON_LIBRARY_DIRS "${GUDHI_CYTHON_LIBRARY_DIRS}'${GMPXX_LIBRARIES_DIR}', ")
       endif(GMPXX_FOUND)
     endif(GMP_FOUND)
@@ -176,8 +184,13 @@ if(CYTHON_FOUND)
   if (TBB_FOUND AND WITH_GUDHI_USE_TBB)
     add_gudhi_debug_info("TBB version ${TBB_INTERFACE_VERSION} found and used")
     set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DGUDHI_USE_TBB', ")
-    add_gudhi_cython_lib(${TBB_RELEASE_LIBRARY})
-    add_gudhi_cython_lib(${TBB_MALLOC_RELEASE_LIBRARY})
+    if(CMAKE_BUILD_TYPE MATCHES Debug)
+      add_gudhi_cython_lib("${TBB_DEBUG_LIBRARY}")
+      add_gudhi_cython_lib("${TBB_MALLOC_DEBUG_LIBRARY}")
+    else()
+      add_gudhi_cython_lib("${TBB_RELEASE_LIBRARY}")
+      add_gudhi_cython_lib("${TBB_MALLOC_RELEASE_LIBRARY}")
+    endif()
     set(GUDHI_CYTHON_LIBRARY_DIRS "${GUDHI_CYTHON_LIBRARY_DIRS}'${TBB_LIBRARY_DIRS}', ")
     set(GUDHI_CYTHON_INCLUDE_DIRS "${GUDHI_CYTHON_INCLUDE_DIRS}'${TBB_INCLUDE_DIRS}', ")
   endif()